...
| Code Block |
|---|
#!/bin/bash -l
#PBS -N VirReport
#PBS -l select=1:ncpus=2:mem=8gb
#PBS -l walltime=05:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run eresearchqut/VirReport -profile singularity -resume --indexfile index.csv \
--merge_lane --qualityfilter --rna_source_profile \
--bowtie_db_dir /path_to_bowtie_indices \
--dedup \
--virreport_ncbi --blast_viral_db_path /path_to_ncbi_databases \
--deteciondetection_reporting_nt |
Example 3:
In the PBS job below, homology searches will be run against NCBI and the PVirDB. The pipeline will also run VirusDetect in parallel.
| Code Block | ||
|---|---|---|
| ||
#!/bin/bash -l
#PBS -N VirReport
#PBS -l select=1:ncpus=2:mem=8gb
#PBS -l walltime=05:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run eresearchqut/VirReport -profile singularity -resume --indexfile index.csv \
--merge_lane --qualityfilter --rna_source_profile \
--bowtie_db_dir /path_to_bowtie_indices \
--dedup \
--virreport_ncbi --blast_viral_db_path /path_to_ncbi_databases --detecion_reporting_viral_nt \
--virreport_viral_db --blast_viral_db_path /path_to_local_viral_database --deteciondetection_reporting_viral_db \
--virusdetect --virusdetect_db_path
sampleid,samplepath
MT500,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/ELL11002/ELL11002A3/MT500_S3_L001_R1_001.fastq.gz
MT500,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/ELL11002/ELL11002A3/MT500_S3_L002_R1_001.fastq.gz
MT502,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/ELL11002/ELL11002A5/MT502_S5_L001_R1_001.fastq.gz
MT502,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/ELL11002/ELL11002A5/MT502_S5_L002_R1_001.fastq.gz
MT512,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A1/Fn1_S25_L001_R1_001.fastq.gz
MT512,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A1/Fn1_S25_L002_R1_001.fastq.gz
MT524,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A13/FraD3_S28_L001_R1_001.fastq.gz
MT524,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A13/FraD3_S28_L002_R1_001.fastq.gz
CT113,/work/hia_mt18005/raw_data/20220629_RAMACIOTTI_DES10730/DES10730A20/CT_113_S20_L001_R1_001.fastq.gz
CT113,/work/hia_mt18005/raw_data/20220629_RAMACIOTTI_DES10730/DES10730A20/CT_113_S20_L002_R1_001.fastq.gz
CT140,/work/hia_mt18005/raw_data/20220629_RAMACIOTTI_DES10730/DES10730A47/CT_140_S47_L001_R1_001.fastq.gz
CT140,/work/hia_mt18005/raw_data/20220629_RAMACIOTTI_DES10730/DES10730A47/CT_140_S47_L002_R1_001.fastq.gz
MT515,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A4/Cn1_S19_L001_R1_001.fastq.gz
MT515,/work/hia_mt18005/raw_data/20220915_RAMACIOTTI_ELL11002_LEL11109/LEL11109/LEL11109A4/Cn1_S19_L002_R1_001.fastq.gz
MT005,/work/hia_mt18005/raw_data/20210618_RAMACIOTTI_ELL9278/ELL9278/ELL9278A04/MT005_S4_L001_R1_001.fastq.gz
MT005,/work/hia_mt18005/raw_data/20210618_RAMACIOTTI_ELL9278/ELL9278/ELL9278A04/MT005_S4_L002_R1_001.fastq.gz
2223PEQ041,/work/hia_mt18005/raw_data/20221018_RAMACIOTTI_LEL11294/LEL11294/LEL11294A15/2223PEQ041_S15_L001_R1_001.fastq.gz
2223PEQ041,/work/hia_mt18005/raw_data/20221018_RAMACIOTTI_LEL11294/LEL11294/LEL11294A15/2223PEQ041_S15_L002_R1_001.fastq.gz
MT447,/work/hia_mt18005/raw_data/20220218_RAMACIOTTI_LEL10024/MT447_S40_L001_R1_001.fastq.gz
MT447,/work/hia_mt18005/raw_data/20220218_RAMACIOTTI_LEL10024/MT447_S40_L002_R1_001.fastq.gz
MT449,/work/hia_mt18005/raw_data/20220218_RAMACIOTTI_LEL10024/MT449_S33_L001_R1_001.fastq.gz
MT449,/work/hia_mt18005/raw_data/20220218_RAMACIOTTI_LEL10024/MT449_S33_L002_R1_001.fastq.gz
2223PEQ012,/work/hia_mt18005/raw_data/20221018_RAMACIOTTI_LEL11291/LEL11291/LEL11291A12/2223PEQ012_S12_L001_R1_001.fastq.gz
2223PEQ012,/work/hia_mt18005/raw_data/20221018_RAMACIOTTI_LEL11291/LEL11291/LEL11291A12/2223PEQ012_S12_L002_R1_001.fastq.gz |
...